SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences.

Single-exon coding sequences (CDSs), also known as 'single-exon genes' (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases. Database URL: http://v2.sinex.cl/.

Evaluation of Lower-Dose Spiral Head CT for Detection of Intracranial Findings Causing Neurologic Deficits.

BACKGROUND AND PURPOSE: Despite the frequent use of unenhanced head CT for the detection of acute neurologic deficit, the radiation dose for this exam varies widely. Our aim was to evaluate the performance of lower-dose head CT for detection of intracranial findings resulting in acute neurologic deficit. MATERIALS AND METHODS: Projection data from 83 patients undergoing unenhanced spiral head CT for suspected neurologic deficits were collected. Cases positive for infarction, intra-axial hemorrhage, mass, or extra-axial hemorrhage required confirmation by histopathology, surgery, progression of findings, or corresponding neurologic deficit; cases negative for these target diagnoses required negative assessments by two neuroradiologists and a clinical neurologist. A routine dose head CT was obtained using 250 effective mAs and iterative reconstruction. Lower-dose configurations were reconstructed (25-effective mAs iterative reconstruction, 50-effective mAs filtered back-projection and iterative reconstruction, 100-effective mAs filtered back-projection and iterative reconstruction, 200-effective mAs filtered back-projection). Three neuroradiologists circled findings, indicating diagnosis, confidence (0-100), and image quality. The difference between the jackknife alternative free-response receiver operating characteristic figure of merit at routine and lower-dose configurations was estimated. A lower 95% CI estimate of the difference greater than -0.10 indicated noninferiority. RESULTS: Forty-two of 83 patients had 70 intracranial findings (29 infarcts, 25 masses, 10 extra- and 6 intra-axial hemorrhages) at routine head CT (CT dose index = 38.3 mGy). The routine-dose jackknife alternative free-response receiver operating characteristic figure of merit was 0.87 (95% CI, 0.81-0.93). Noninferiority was shown for 100-effective mAs iterative reconstruction (figure of merit difference, -0.04; 95% CI, -0.08 to 0.004) and 200-effective mAs filtered back-projection (-0.02; 95% CI, -0.06 to 0.02) but not for 100-effective mAs filtered back-projection (-0.06; 95% CI, -0.10 to -0.02) or lower-dose levels. Image quality was better at higher-dose levels and with iterative reconstruction (P < .05). CONCLUSIONS: Observer performance for dose levels using 100-200 eff mAs was noninferior to that observed at 250 effective mAs with iterative reconstruction, with iterative reconstruction preserving noninferiority at a mean CT dose index of 15.2 mGy.

Hypertension and aging in rural Haiti: results from a preliminary survey.

Cross-sectional studies in the developed countries document strong relationships among age, systolic blood pressure (SBP) and pulse pressure (PP). There is little information about these trends and their impact in underdeveloped countries with different socioeconomic and lifestyle characteristics. We studied a convenience sample of 572 residents of rural Fontaine, Haiti: 193 males and 379 females (mean, s.d.) age 40.2 (17.1) years and performed intake questionnaires and BP measurements in participants' homes. Income and educational achievement were very low but most-recommended lifestyle factors were very favorable: very high physical activity, low dietary fat, virtually no obesity (body mass index 21.8 (4.9)), and low smoking prevalence. Rough estimates of salt intake were high (~13 g per day) as was the overall prevalence of hypertension: 34.4% (23.4% in males, 40.2% in females). SBP and PP were related closely to age (r2=0.28, P<0.001 and r2=0.22, P<0.001); for each decade of age, SBP increased by 7.6 mm Hg. Diastolic BP peaked in the 6th decade (polynomial r2=0.22, P<0.001) and the nadir of PP occurred in the 3rd decade. We conclude that, despite a favorable profile of lifestyle characteristics and no obesity, the prevalence of hypertension and rate of increase in SBP and PP with age in Haiti are at least as high as those of developed countries.

International comparisons of the management of patients with non-ST segment elevation acute myocardial infarction in the United Kingdom, Sweden, and the United States: The MINAP/NICOR, SWEDEHEART/RIKS-HIA, and ACTION Registry-GWTG/NCDR registries.

OBJECTIVES: To compare management of patients with acute non-ST segment elevation myocardial infarction (NSTEMI) in three developed countries with national ongoing registries. BACKGROUND: Results from clinical trials suggest significant variation in care across the world. However, international comparisons in "real world" registries are limited. METHODS: We compared the use of in-hospital procedures and discharge medications for patients admitted with NSTEMI from 2007 to 2010 using the unselective MINAP/NICOR [England and Wales (UK); n=137,009], the unselective SWEDEHEART/RIKS-HIA (Sweden; n=45,069), and the selective ACTION Registry-GWTG/NCDR [United States (US); n=147,438] clinical registries. RESULTS: Patients enrolled among the three registries were generally similar except those in the US who were younger but had higher rates of smoking, diabetes, hypertension, prior heart failure, and prior MI than in Sweden or in UK. Angiography and percutaneous coronary intervention (PCI) were performed more often in the US (76% and 44%) and Sweden (65% and 42%) relative to the UK (32% and 22%). Discharge betablockers were also prescribed more often in the US (89%) and Sweden (89%) than in the UK (76%). In contrast, discharge statins, angiotensin converting enzyme inhibitors/angiotensin receptor blockers (ACEI/ARB), and dual antiplatelet agents (among those not receiving PCI) were higher in the UK (92%, 79%, and 71%) than in the US (85%, 65%, 41%) and Sweden (81%, 69%, and 49%). CONCLUSIONS: The care for patients with NSTEMI differed substantially among the three countries. These differences in care among countries provide an opportunity for future comparative effectiveness research as well as identify opportunities for global quality improvement.

Is postal postoperative follow-up in urogynaecology feasible?

Postoperative follow-up after urogynaecological surgery has been little investigated. Traditionally, it is done in hospital but there is wide variation in the assessments and timing. We aimed to determine the viability of postal follow-up in women undergoing urogynaecological surgery. This is a retrospective review of prospectively collected data. All women who underwent prolapse and/or urinary incontinence surgery between January and June 2010 were included. Validated ICIQ questionnaires for prolapse and/or incontinence, as appropriate, were used, before surgery and at 6 months postoperatively. The primary outcome was the response rate to postal follow-up. A total of 70 women had urogynaecology surgery during the study period; 65 (93%) women returned the questionnaires (95% CI 84-97%, p < 0.0001). The postoperative questionnaires scores showed a statistically significant improvement compared with the preoperative scores. This results in only a small proportion of women needing hospital attendance for follow-up (10%). We conclude that postal follow-up is feasible.

Comparison of calibrated and uncalibrated bone mineral density by CT to DEXA in menopausal women.

OBJECTIVES: Coronary artery disease and osteoporosis increase in women after menopause. Computed tomography (CT) scans of the heart used to evaluate coronary arterial calcification include images of the thoracic vertebrae. The utility of using these images to assess bone health in women remains to be defined. Analyses of thoracic spine volumetric bone mineral density (vBMD) from CT scans of the heart were performed to determine how specific calibration affects the ability to assess vBMD in recently menopausal women and to evaluate how vBMD relates to areal bone mineral density (aBMD) using dual-energy X-ray absorptiometry (DEXA). METHODS: Women (n = 111) enrolled in the Kronos Early Estrogen Prevention Study (KEEPS) at Mayo Clinic underwent a CT scan of the heart that included calibration phantoms and a DEXA of the lumbar spine. The Spine Cancer Assessment program was used to determine vBMD of thoracic vertebrae with and without the calibration correction. RESULTS: Trabecular bone vBMD at T8 averaged 163.57±28.58 and 157.94±27.55 mg/cc (mean±standard deviation, SD) for calibrated and uncalibrated values, respectively. The relationship between calibrated and uncalibrated measures approached unity (R = 0.98). Lumbar spine (L2-4) aBMD was 1.19±0.16 g/cm(2) (mean±SD). Both calibrated and uncalibrated thoracic vBMD correlated positively and significantly with lumbar aBMD, but the relationship was less than unity (R = 0.63). CONCLUSION: Uncalibrated measures of thoracic spine vBMD obtained from CT scans of the heart may provide clinically relevant information about bone health and osteoporosis/osteopenia risk in recently menopausal women.

Coronary arterial calcification and thoracic spine mineral density in early menopause.

OBJECTIVES: Cardiovascular disease and osteoporosis increase in women after menopause. While aortic calcification is associated with bone loss in women, a similar relationship for coronary arterial calcification (CAC), a risk factor for coronary artery disease in women, is less clear. This study was designed to examine the relationship between CAC and volumetric bone mineral density (vBMD) in women (n=137) who were within a median of 18 months past their last menses at screening for the Kronos Early Estrogen Prevention Study (KEEPS). METHODS: CAC was measured using 64-slice computed tomography; vBMD was measured from these images using the Spine Cancer Assessment program. Concentrations of osteocalcin, bone alkaline phosphatase, tartrate-resident acid phosphatase-5b and osteopontin as bone matrix protein in serum and plasma were evaluated by ELISA. RESULTS: CAC scores ranged from 0 to 327.6 Agatston Units (AU); 113 women had a score of 0 AU, 20 had a CAC score between 0 and 50 AU, and four had a CAC score>50 AU. Although not statistically significant, there was a trend toward decreasing central density of thoracic T9 with increasing CAC. On average, levels of markers of bone turnover were within the normal range but did not correlate with age or with months past menopause. CONCLUSIONS: Clinically significant CAC and spine vBMD are quantifiable from the same scans within the first 3 years of menopause. Additional work is needed to determine how these measurements change with increasing age or with estrogenic treatments.

An event-driven distributed processing architecture for image-guided cardiac ablation therapy.

Medical imaging data is becoming increasing valuable in interventional medicine, not only for preoperative planning, but also for real-time guidance during clinical procedures. Three key components necessary for image-guided intervention are real-time tracking of the surgical instrument, aligning the real-world patient space with image-space, and creating a meaningful display that integrates the tracked instrument and patient data. Issues to consider when developing image-guided intervention systems include the communication scheme, the ability to distribute CPU intensive tasks, and flexibility to allow for new technologies. In this work, we have designed a communication architecture for use in image-guided catheter ablation therapy. Communication between the system components is through a database which contains an event queue and auxiliary data tables. The communication scheme is unique in that each system component is responsible for querying and responding to relevant events from the centralized database queue. An advantage of the architecture is the flexibility to add new system components without affecting existing software code. In addition, the architecture is intrinsically distributed, in that components can run on different CPU boxes, and even different operating systems. We refer to this Framework for Image-Guided Navigation using a Distributed Event-Driven Database in Real-Time as the FINDER architecture. This architecture has been implemented for the specific application of image-guided cardiac ablation therapy. We describe our prototype image-guidance system and demonstrate its functionality by emulating a cardiac ablation procedure with a patient-specific phantom. The proposed architecture, designed to be modular, flexible, and intuitive, is a key step towards our goal of developing a complete system for visualization and targeting in image-guided cardiac ablation procedures.

Patient specific physical anatomy models.

The advent of small footprint stereo-lithographic printers and the ready availability of segmentation and surface modeling software provide a unique opportunity to create patient-specific physical models of anatomy, validation of image guided intervention applications against phantoms that exhibit naturally occurring anatomic variation. Because these models can incorporate all structures relevant to a procedure, this allows validation to occur under realistic conditions using the same or similar techniques as would be used in a clinical application. This in turn reduces the number of trials and time spent performing in-vivo validation experiments. In this paper, we describe our general approach for the creation of both non-tissue and tissue-mimicking patient-specific models as part of a general-purpose patient emulation system used to validate image guided intervention applications.

Twelve-week monotherapy with the DPP-4 inhibitor vildagliptin improves glycemic control in subjects with type 2 diabetes.

UNLABELLED: Inhibition of dipeptidyl peptidase-4 enhances the activity of incretin hormones, improving glycemic control in subjects with type 2 diabetes. This twelve-week randomized, double-masked, placebo-controlled study assessed the efficacy and tolerability of the specific and potent oral dipeptidyl peptidase-4 inhibitor, vildagliptin (25 mg, bid, n=70) VS. placebo (bid, n=28) in previously diet-treated subjects with type 2 diabetes. Standardized meal tests were performed at baseline and endpoint. The between-group difference in adjusted mean change in HbA1c from baseline to endpoint was - 0.6 +/- 0.2 % (p=0.0012) for the whole cohort (baseline 8.0 %) and -1.2 % for subjects with baseline HbA1c 8.0 - 9.5 %. Fasting glucose and mean prandial glucose were reduced by 1.1 +/- 0.4 (p=0.0043) and 1.9 +/- 0.5 mmol/l (p <0.0001), respectively. The between-group differences in corrected insulin response at peak glucose and mean prandial C-peptide were + 0.06 +/- 0.02 (p=0.0258) and + 0.10 +/- 0.03 nmol/l (p=0.0031), respectively. Vildagliptin had no effect on fasting lipid levels or body weight. The incidence of adverse events was similar in subjects receiving placebo (71.4 %) and vildagliptin (55.7 %). CONCLUSION: monotherapy with vildagliptin is well tolerated and improves glycemic control in diet-treated subjects with type 2 diabetes. Concomitant improvements in beta-cell function were also observed. Subjects with higher baseline HbA1c levels showed greater response.

An integrated system for real-time image guided cardiac catheter ablation.

Minimally invasive cardiac catheter ablation procedures require effective visualization of the relevant heart anatomy and electrophysiology (EP). In a typical ablation procedure, the visualization tools available to the cardiologist include bi-plane fluoroscopy, real-time ultrasound, and a coarse 3D model which gives a rough representation of cardiac anatomy and electrical activity. Recently, there has been increased interest in incorporating detailed, patient specific anatomical data into the cardiac ablation procedure. We are currently developing a prototype system which both integrates a patient specific, preoperative data model into the procedure as well as fuses the various visualization modalities (i.e. fluoroscopy, ultrasound, EP) into a single display. In this paper, we focus on two aspects of the prototype system. First, we describe the framework for integrating the various system components, including an efficient communication protocol. Second, using a simple two-chamber phantom of the heart, we demonstrate the ability to integrate preoperative data into the ablation procedure. This involves the registration and visualization of tracked catheter points within the cardiac chambers of the preoperative model.

Sperm banking in adolescent cancer patients.

BACKGROUND: Semen cryopreservation is a widely available method of maintaining fertility in male cancer patients. However this facility is not always used. AIMS: To identify the barriers to successful sperm banking in a group of adolescent and young adult patients. METHODS: Questionnaires were administered to 55 patients aged 13-21 years who had received potentially gonadotoxic therapy between 1997 and 2001 and had been offered sperm banking. RESULTS: Forty five questionnaires were completed; 67% of respondents were able to bank sperm. Those who had been unsuccessful were younger and described higher levels of anxiety at diagnosis and greater difficulty in talking about fertility. They also described less understanding of sperm banking at the time of diagnosis. CONCLUSION: Most adolescent cancer patients who have been offered fertility preservation are able to bank sperm. Younger patients may be helped by the provision of high quality information and more open discussion of the technique.

Improved glycaemic control with dipeptidyl peptidase-4 inhibition in patients with type 2 diabetes: vildagliptin (LAF237) dose response.

OBJECTIVE: A novel treatment option for diabetic patients is the enhancement of incretin hormone activity by inhibition of the enzyme dipeptidyl peptidase-4 (DPP-4). This study was designed to establish a dose of the DPP-4-inhibitor vildagliptin (LAF237) that was effective in reducing HbA1c levels and was safe and well tolerated in patients with type 2 diabetes. PATIENTS AND METHODS: The study of 279 patients with type 2 diabetes consisted of a 4-week run-in phase where patients received placebo and a 12-week active treatment phase where they received one of the following dosages of vildagliptin: 25 mg twice daily, 25, 50 or 100 mg once daily (qd), or placebo. RESULTS: There was a statistically significant reduction in HbA1c levels in the vildagliptin 50 mg qd (p=0.003) and 100 mg qd groups (p=0.004) compared with the placebo group. The mean 4-h postprandial glucose level was significantly reduced from placebo in the vildagliptin 50 mg qd group (p = 0.012) and mean 4-h postprandial insulin was significantly increased from baseline vs. placebo in the vildagliptin 100 mg qd group (p=0.022). The assessment of beta-cell function (HOMA-B) was significantly increased in the vildagliptin 100 mg qd treatment group (p=0.007). The incidence of adverse events was similar in all treatment groups including placebo. CONCLUSIONS: Vildagliptin, at 50 and 100 mg qd, was effective in reducing HbA1c levels compared with placebo in patients with type 2 diabetes. Vildagliptin at dosages up to 100 mg qd appeared safe and well tolerated.

The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans.

Acidithiobacillus ferrooxidans is a Gram-negative bacterium that lives at pH 2 in high concentrations of soluble ferrous and ferric iron, making it an interesting model for understanding the biological mechanisms of bacterial iron uptake and homeostasis in extremely acid conditions. A candidate fur(AF) (Ferric Uptake Regulator) gene was identified in the A. ferrooxidans ATCC 23270 genome. Fur(AF) has significant sequence similarity, including conservation of functional motifs, to known Fur orthologues and exhibits cross-reactivity to Escherichia coli Fur antiserum. The fur(AF) gene is able to complement fur deficiency in E. coli in an iron-responsive manner. Fur(AF) is also able to bind specifically to E. coli Fur regulatory regions (Fur boxes) and to a candidate Fur box from A. ferrooxidans, as judged by electrophoretic mobility shift assays. Fur(AF) represses gene expression from E. coli Fur-responsive promoters fiu and fhuF when expressed at high protein levels. However, it increases gene expression from these promoters at low concentrations and possibly from other Fur-regulated promoters involved in iron-responsive oxidative stress responses.

Marrow stromal cells from patients affected by MPS I differentially support haematopoietic progenitor cell development.

Bone marrow transplantation is the therapy of choice in patients affected by MPS I (Hurler syndrome), but a high incidence of rejection limits the success of this treatment. The deficiency of alpha-L-iduronidase (EC 1.2.3.76), one of the enzymes responsible for the degradation of glycosaminoglycans, results in accumulation of heparan and dermatan sulphate in these patients. Heparan sulphate and dermatan sulphate are known to be important components of the bone marrow microenvironment and critical for haematopoietic cell development. In this study we compared the ability of marrow stromal cells from MPS I patients and healthy donors to support normal haematopoiesis in Dexter-type long term culture. We found an inverse stroma/supernatant ratio in the number of clonogenic progenitors, particularly the colony-forming unit granulocyte-machrophage in MPS I cultures when compared to normal controls. No alteration in the adhesion of haematopoietic cells to the stroma of MPS I patients was found, suggesting that the altered distribution in the number of clonogenic progenitors is probably the result of an accelerated process of differentiation and maturation. The use of alpha-L-iduronidase gene-corrected marrow stromal cells re-established normal haematopoiesis in culture, suggesting that correction of the bone marrow microenvironment with competent enzyme prior to transplantation might help establishment of donor haematopoiesis.

Efficient replication by herpes simplex virus type 1 involves activation of the IkappaB kinase-IkappaB-p65 pathway.

Infection by herpes simplex virus type 1 (HSV-1) induces a persistent nuclear translocation of NFkappaB. To identify upstream effectors of NFkappaB and their effect on virus replication, we employed mouse embryo fibroblast (MEF)-derived cell lines with deletions of either IKK1 or IKK2, the catalytic subunits of the IkappaB kinase (IKK) complex. Infected MEFs were assayed for virus yield, loss of IkappaBalpha, nuclear translocation of p65, and NFkappaB DNA-binding activity. Absence of either IKK1 or IKK2 resulted in an 86 to 94% loss of virus yield compared to that of normal MEFs, little or no loss of IkappaBalpha, and greatly reduced NFkappaB nuclear translocation. Consistent with reduced virus yield, accumulation of the late proteins VP16 and gC was severely depressed. Infection of normal MEFs, Hep2, or A549 cells with an adenovirus vector expressing a dominant-negative (DN) IkappaBalpha, followed by superinfection with HSV, resulted in a 98% drop in virus yield. These results indicate that the IKK-IkappaB-p65 pathway activates NFkappaB after virus infection. Analysis of NFkappaB activation and virus replication in control and double-stranded RNA-activated protein kinase-null MEFs indicated that this kinase plays no role in the NFkappaB activation pathway. Finally, in cells where NFkappaB was blocked because of DNIkappaB expression, HSV failed to suppress two markers of apoptosis, cell surface Annexin V staining and PARP cleavage. These results support a model in which activation of NFkappaB promotes efficient replication by HSV, at least in part by suppressing a host innate response to virus infection.

Comparative outcomes of percutaneous coronary interventions in diabetics vs non-diabetics with prior coronary artery bypass grafting.

AIMS: To determine the influence of diabetes on outcome after percutaneous coronary intervention in patients with prior coronary artery bypass grafting. METHODS AND RESULTS: Patients with prior coronary artery bypass grafting undergoing percutaneous coronary intervention from 1 January 1996, to 31 August 2000, were divided into two groups based on whether or not they had diabetes, excluding patients with acute infarction or shock. Cox proportional hazards models were utilized to estimate the association between diabetes and adverse events. One thousand one hundred and fifty-three post-coronary artery bypass grafting percutaneous coronary intervention patients were identified (326 diabetics and 827 non-diabetics). Diabetics were younger, more likely to have hypertension, heart failure, and lower ejection fraction. Procedural characteristics and angiographic and procedural success rates were similar. Diabetes was associated with increased mortality (hazard ratio 1.58, 95% confidence intervals 1.10-2.27). Diabetes did not have a significant effect on mortality in patients treated for single-territory coronary disease (hazard ratio 1.44, 95% confidence intervals 0.69-3.02), but did in patients with multi-territory disease (hazard ratio 1.79, 95% confidence intervals 1.16-2.76). However, in diabetics with multi-territory disease who were completely revascularized with percutaneous coronary intervention, mortality was comparable to non-diabetics (hazard ratio 1.32, 95% confidence intervals 0.57-3.03). CONCLUSION: Among percutaneous coronary intervention patients with prior coronary artery bypass grafting, diabetes portends an adverse prognosis.

Outcomes of patients with chronic renal insufficiency in the bypass angioplasty revascularization investigation.

BACKGROUND: Although severe chronic kidney disease (CKD) is an independent predictor of mortality among patients with coronary artery disease, the impact of mild CKD on morbidity and mortality has not been fully defined. METHODS AND RESULTS: Morbidity and mortality for the 3608 patients with multivessel coronary artery disease enrolled in the Bypass Angioplasty Revascularization Investigation randomized trial and registry were compared on the basis of the presence and absence of CKD, defined as a preprocedure serum creatinine level of >1.5 mg/dL. Seventy-six patients had CKD. Patients with renal insufficiency were older and more likely to have a history of diabetes, hypertension, and other comorbidities. Among patients undergoing PTCA, patients with CKD had a greater frequency of in-hospital death and cardiogenic shock (P<0.05 and 0.01, respectively). There was a trend toward a larger proportion of patients with CKD experiencing angina at 5 years (P=0.079). Patients with CKD had more cardiac admissions (P=0.003 and <0.0001 for patients undergoing PTCA and CABG, respectively) and a shorter time to subsequent CABG after initial revascularization than patients without CKD (P=0.01). CKD was associated with a higher risk of death at 7 years, both of all causes (relative risk 2.2, P<0.001) and of cardiac causes (relative risk 2.8, P<0.001). CONCLUSIONS: CKD is associated with an increased risk of recurrent hospitalization, subsequent CABG, and mortality. This increased risk of death is independent of and additive to the risk associated with diabetes.